In waldronlab/MultiAssayExperimentData: Exposes and Makes Available Data from the cBioPortal Web Resources

knitr::opts_chunk$set(cache = TRUE)

Installation

Please use the devel version of the AnVIL Bioconductor package.

library(cBioPortalData)
library(AnVIL)

Introduction

The cBioPortal for Cancer Genomics website is a great resource for interactive exploration of study datasets. However, it does not easily allow the analyst to obtain and further analyze the data.

We've developed the cBioPortalData package to fill this need to programmatically access the data resources available on the cBioPortal.

The cBioPortalData package provides an R interface for accessing the cBioPortal study data within the Bioconductor ecosystem.

It downloads study data from the cBioPortal API (https://cbioportal.org/api) and uses Bioconductor infrastructure to cache and represent the data.

We use the MultiAssayExperiment (@Ramos2017-er) package to integrate, represent, and coordinate multiple experiments for the studies availble in the cBioPortal. This package in conjunction with curatedTCGAData give access to a large trove of publicly available bioinformatic data. Please see our publication here (@Ramos2020-ya).

We demonstrate common use cases of cBioPortalData and curatedTCGAData during Bioconductor conference workshops.

Overview

This vignette is for users / developers who would like to learn more about the available data in cBioPortalData and to learn how to hit other endpoints in the cBioPortal API implementation. The functionality demonstrated here is used internally by the package to create integrative representations of study datasets.

Note. To avoid overloading the API service, the API was designed to only query a part of the study data. Therefore, the user is required to enter either a set of genes of interest or a gene panel identifier.

API representation

Obtaining the cBioPortal API representation object

(cbio <- cBioPortal())

Operations

Check available tags, operations, and descriptions as a tibble:

tags(cbio)
head(tags(cbio)$operation)

Searching through the API

searchOps(cbio, "clinical")

Studies

Get the list of studies available:

getStudies(cbio)

Clinical Data

Obtain the clinical data for a particular study:

clinicalData(cbio, "acc_tcga")

Molecular Profiles

A table of molecular profiles for a particular study can be obtained by running the following:

mols <- molecularProfiles(cbio, "acc_tcga")
mols[["molecularProfileId"]]

Molecular Profile Data

The data for a molecular profile can be obtained with prior knowledge of available entrezGeneIds:

molecularData(cbio, molecularProfileIds = "acc_tcga_rna_seq_v2_mrna",
    entrezGeneIds = c(1, 2),
    sampleIds = c("TCGA-OR-A5J1-01",  "TCGA-OR-A5J2-01")
)

Genes

All available genes

A list of all the genes provided by the API service including hugo symbols, and entrez gene IDs can be obtained by using the geneTable function:

geneTable(cbio)

Gene Panels

genePanels(cbio)
getGenePanel(cbio, "IMPACT341")

Molecular Gene Panels

genePanelMolecular

gprppa <- genePanelMolecular(cbio,
    molecularProfileId = "acc_tcga_rppa",
    sampleListId = "acc_tcga_all")
gprppa

getGenePanelMolecular

getGenePanelMolecular(cbio,
    molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_gistic"),
    sampleIds = allSamples(cbio, "acc_tcga")$sampleId
)

getDataByGenes

getDataByGenes(cbio, "acc_tcga", genePanelId = "IMPACT341",
    molecularProfileIds = "acc_tcga_rppa", sampleListId = "acc_tcga_rppa")

It uses the getAllGenesUsingGET function from the API.

Samples

Sample List Identifiers

To display all available sample list identifiers for a particular study ID, one can use the sampleLists function:

sampleLists(cbio, "acc_tcga")

Sample Identifiers

One can obtain the barcodes / identifiers for each sample using a specific sample list identifier, in this case we want all the copy number alteration samples:

samplesInSampleLists(cbio, "acc_tcga_cna")

This returns a CharacterList of all identifiers for each sample list identifier input:

samplesInSampleLists(cbio, c("acc_tcga_cna", "acc_tcga_cnaseq"))

All samples within a study ID

allSamples(cbio, "acc_tcga")

Info on Samples

getSampleInfo(cbio, studyId = "acc_tcga",
    sampleListIds = c("acc_tcga_rppa", "acc_tcga_cna"))

Advanced Usage

The cBioPortal API representation is not limited to the functions provided in the package. Users who wish to make use of any of the endpoints provided by the API specification should use the dollar sign $ function to access the endpoints.

First the user should see the input for a particular endpoint as detailed in the API:

cbio$getGeneUsingGET

Then the user can provide such input:

(resp <- cbio$getGeneUsingGET("BRCA1"))

which will require the user to 'translate' the response using httr::content:

httr::content(resp)

Clearing the cache

For users who wish to clear the entire cBioPortalData cache, it is recommended that they use:

unlink("~/.cache/cBioPortalData/")

sessionInfo

sessionInfo()

waldronlab/MultiAssayExperimentData documentation built on May 4, 2024, 2:29 p.m.